Seroatlas · Human Serome Atlas

SCN11A

Sodium channel protein type 11 subunit alpha

Also known as: NaN, Nav1.9, SCN12A, SCNBA_HUMAN, SNS-2

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q9UI33
Gene: SCN11A
Ensembl: ENSG00000168356
Chromosome: 3
Canonical length: 1791 aa
Protein class: Disease related genes, FDA approved drug targets, Human disease related genes, Predicted membrane proteins, Transporters, Voltage-gated ion channels

OverviewNCBI Gene

Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with 24 transmembrane domains and one or more regulatory beta subunits. They are responsible for the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family, and is highly expressed in nociceptive neurons of dorsal root ganglia and trigeminal ganglia. It mediates brain-derived neurotrophic factor-evoked membrane depolarization and is a major effector of peripheral inflammatory pain hypersensitivity. Mutations in this gene have been associated with hereditary sensory and autonomic neuropathy type VII and familial episodic pain syndrome-3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2017]

Canonical amino-acid sequenceUniProt

1791 residues, UniProt reviewed canonical sequence.

>Q9UI33|SCN11A
     1  MDDRCYPVIF PDERNFRPFT SDSLAAIEKR IAIQKEKKKS KDQTGEVPQP RPQLDLKASR
    61  KLPKLYGDIP RELIGKPLED LDPFYRNHKT FMVLNRKRTI YRFSAKHALF IFGPFNSIRS
   121  LAIRVSVHSL FSMFIIGTVI INCVFMATGP AKNSNSNNTD IAECVFTGIY IFEALIKILA
   181  RGFILDEFSF LRDPWNWLDS IVIGIAIVSY IPGITIKLLP LRTFRVFRAL KAISVVSRLK
   241  VIVGALLRSV KKLVNVIILT FFCLSIFALV GQQLFMGSLN LKCISRDCKN ISNPEAYDHC
   301  FEKKENSPEF KMCGIWMGNS ACSIQYECKH TKINPDYNYT NFDNFGWSFL AMFRLMTQDS
   361  WEKLYQQTLR TTGLYSVFFF IVVIFLGSFY LINLTLAVVT MAYEEQNKNV AAEIEAKEKM
   421  FQEAQQLLKE EKEALVAMGI DRSSLTSLET SYFTPKKRKL FGNKKRKSFF LRESGKDQPP
   481  GSDSDEDCQK KPQLLEQTKR LSQNLSLDHF DEHGDPLQRQ RALSAVSILT ITMKEQEKSQ
   541  EPCLPCGENL ASKYLVWNCC PQWLCVKKVL RTVMTDPFTE LAITICIIIN TVFLAMEHHK
   601  MEASFEKMLN IGNLVFTSIF IAEMCLKIIA LDPYHYFRRG WNIFDSIVAL LSFADVMNCV
   661  LQKRSWPFLR SFRVLRVFKL AKSWPTLNTL IKIIGNSVGA LGSLTVVLVI VIFIFSVVGM
   721  QLFGRSFNSQ KSPKLCNPTG PTVSCLRHWH MGDFWHSFLV VFRILCGEWI ENMWECMQEA
   781  NASSSLCVIV FILITVIGKL VVLNLFIALL LNSFSNEERN GNLEGEARKT KVQLALDRFR
   841  RAFCFVRHTL EHFCHKWCRK QNLPQQKEVA GGCAAQSKDI IPLVMEMKRG SETQEELGIL
   901  TSVPKTLGVR HDWTWLAPLA EEEDDVEFSG EDNAQRITQP EPEQQAYELH QENKKPTSQR
   961  VQSVEIDMFS EDEPHLTIQD PRKKSDVTSI LSECSTIDLQ DGFGWLPEMV PKKQPERCLP
  1021  KGFGCCFPCC SVDKRKPPWV IWWNLRKTCY QIVKHSWFES FIIFVILLSS GALIFEDVHL
  1081  ENQPKIQELL NCTDIIFTHI FILEMVLKWV AFGFGKYFTS AWCCLDFIIV IVSVTTLINL
  1141  MELKSFRTLR ALRPLRALSQ FEGMKVVVNA LIGAIPAILN VLLVCLIFWL VFCILGVYFF
  1201  SGKFGKCING TDSVINYTII TNKSQCESGN FSWINQKVNF DNVGNAYLAL LQVATFKGWM
  1261  DIIYAAVDST EKEQQPEFES NSLGYIYFVV FIIFGSFFTL NLFIGVIIDN FNQQQKKLGG
  1321  QDIFMTEEQK KYYNAMKKLG SKKPQKPIPR PLNKCQGLVF DIVTSQIFDI IIISLIILNM
  1381  ISMMAESYNQ PKAMKSILDH LNWVFVVIFT LECLIKIFAL RQYYFTNGWN LFDCVVVLLS
  1441  IVSTMISTLE NQEHIPFPPT LFRIVRLARI GRILRLVRAA RGIRTLLFAL MMSLPSLFNI
  1501  GLLLFLIMFI YAILGMNWFS KVNPESGIDD IFNFKTFASS MLCLFQISTS AGWDSLLSPM
  1561  LRSKESCNSS SENCHLPGIA TSYFVSYIII SFLIVVNMYI AVILENFNTA TEESEDPLGE
  1621  DDFDIFYEVW EKFDPEATQF IKYSALSDFA DALPEPLRVA KPNKYQFLVM DLPMVSEDRL
  1681  HCMDILFAFT ARVLGGSDGL DSMKAMMEEK FMEANPLKKL YEPIVTTTKR KEEERGAAII
  1741  QKAFRKYMMK VTKGDQGDQN DLENGPHSPL QTLCNGDLSS FGVAKGKVHC D

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SCN11A can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Cell surface
Secreted: No
Transmembrane segments: 24
Mean surface accessibility (rSASA): 0.35
Highest tissue expression: 2.8 nTPM

Expression across tissuesHPA

Tissue

spleen: 2.8 nTPM
urinary bladder: 2 nTPM
placenta: 1.8 nTPM
testis: 1.2 nTPM
colon: 0.6 nTPM
amygdala: 0.5 nTPM

Single-cell type

papillary tip epithelial cells: 170 nCPM
undifferentiated spermatogonia: 57 nCPM
early primary spermatocytes: 50 nCPM
bergmann glia: 49 nCPM
astrocytes: 43 nCPM
differentiating spermatogonia: 39 nCPM

Immune cell

basophil: 0 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM
gdT-cell: 0 nTPM
intermediate monocyte: 0 nTPM
MAIT T-cell: 0 nTPM

Brain region

hypothalamus: 1.3 nTPM
midbrain: 1.3 nTPM
amygdala: 1.2 nTPM
hippocampal formation: 1.2 nTPM
pons: 1.1 nTPM
white matter: 1.1 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about SCN11A.

Disease | AllUniProt

Conditions SCN11A is implicated in, by any mechanism.

Neuropathy, hereditary sensory and autonomic, 7 (HSAN7) MIM:615548
Episodic pain syndrome, familial, 3 (FEPS3) MIM:615552

Disease | GeneticClinVar

9 pathogenic / likely-pathogenic of 1,698 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Familial episodic pain syndrome with predominantly lower limb involvement
Hereditary sensory and autonomic neuropathy type 7
Inborn genetic diseases
Congenital sensory neuropathy with selective loss of small myelinated fibers

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.83
gnomAD pLI: 0
gnomAD missense Z: 0.96
DepMap mean gene effect: -0.08
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

voltage-gated sodium channel activity

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads SCN11A as an antibody target. Whether an autoantibody or antibody against SCN11A could matter depends on whether native SCN11A is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SCN11A is annotated at the cell surface, where native SCN11A is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label SCN11A as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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